I run two EQ folders myself and was initially worried about this. However, after some testing it appears that Launchpad funnels the actual account login into one place, but you still are running the eqgame.exe from whichever directory you click on the shortcut from.
So, the only real PITA's with the new launchpad are that since it's now a shared login, it will only ever remember your last login name regardless of which copy of EQ you run. So if you normally ran the same accounts on different copies of eq and it remembered those account names on each instance of EQ, you're hosed now and you'll be typing in all 8 account names each time. Awesome isn't it!
Also another thing is you can't tab to highlight "I Accept" on the EULA now, you have to mouse click it. At least it seems that way so far to me, didn't mess around with it a whole lot.
You CAN however bypass all the gayness of Launchpad, and instead of having 8 shortcuts to "Everquest.exe", just modify your shortcuts to "eqgame.exe" patchme. This will skip Launchpad and go straight into the game. Just remember to run patcher on patch days, or when you think you might be missing files. That means tab highlighted "I Accept" and remembering of account names for each copy of EQ!
So for example, the target of my shortcuts now look like such:
"C:\Program Files\Games\Everquest\eqgame.exe" patchme
Hope that answers your questions,
Joemama